Ching-Chuan Chen's Blogger

Statistics, Machine Learning and Programming

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PyCharm and Cython

Posted on Edited on In Disqus:

這篇文章主要介紹PyCharm跟Cython

先寫下我的檔案架構

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.
+-- main.py
+-- fib
|   +-- __init__.py
|   +-- cfib.c
|   +-- cfib.h
|   +-- fib.pyx
|   +-- setup.py

每一個檔案的用途：

  1. main.py是主程式
  2. __init__.py是套件引用檔案
  3. cfib.c是用c寫成的fib函數
  4. cfib.h是cfib的header檔，供fib.pyx參照
  5. fib.pyx是Cython檔
  6. setup.py則是拿來編譯整個Cython的

cfib.c內容如下：

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#include "cfib.h"

unsigned long fib(unsigned long n) {
    unsigned long a=0, b=1, i, tmp;
    for (i=0; i<n; ++i) {
        tmp = a; a = a + b; b = tmp;
    }
    return a;
}

cfib.h內容如下：

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#ifndef __CFIB_H__
#define __CFIB_H__

unsigned long fib(unsigned long n);

#endif

基本上cfib.c跟cfib.h就是很標準的c程式寫法，就不贅述，主要是拿來比performance用的

下面則是fix.pyx檔案，fib_c是定義引用的c函數

fib_cython是未優化過的cython程式，基本上就是python樣子

fib_cython_optimized是加上型別的cythoin程式

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cdef extern from "cfib.h":
    unsigned long _fib "fib"(unsigned long n)

def fib_c(n):
    ''' Returns the nth Fibonacci number.'''
    return _fib(n)

def fib_cython(n):
    '''Returns the nth Fibonacci number.'''
    a, b = 0, 1
    for i in range(n):
        a, b = a + b, a
    return a

def fib_cython_optimized(unsigned long n):
    '''Returns the nth Fibonacci number.'''
    cdef unsigned long a=0, b=1, i
    for i in range(n):
        a, b = a + b, a
    return a

__init__.py檔案內容：

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from .fib import *

setup.py檔案內容如下：

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from distutils.core import setup, Extension
from Cython.Build import cythonize

setup(ext_modules = cythonize(Extension(name="fib", sources=["cfib.c", "fib.pyx"])))

有了這幾個檔案之後，我們先來設定PyCharm

打開PyCharm，到settings => Tools => External Tools

然後點+，新增一個工具，設定如下：

Porgram設定$ModuleSdkPath$，Arguments設定$FilePath$ build_ext --inplace，Working directory設定$FileDir$

這樣基本上就大功告成了，然後回到Project對setup.py點右鍵，選External Tools，選CythonBuild就可以看到開始跑了

如果設定對的話，就可以看到編譯成功的訊息

最後就可以來跑跑看啦，main.py如下：

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def fib_python(n):
    '''Returns the nth Fibonacci number.'''
    a, b = 0, 1
    for i in range(n):
        a, b = a + b, a
    return a

if __name__ == '__main__':
    print("##### check result #####")
    import fib
    print("fib(47) in python:", fib_python(47))
    print("fib.fib_c(47):", fib.fib_c(47))
    print("fib.fib_cython(47):", fib.fib_cython(47))
    print("fib.fib_cython_optimized(47):", fib.fib_cython_optimized(47))

    print("\n##### performace benchmark #####")
    import timeit
    python_setup = "from __main__ import fib_python"
    cython_setup = "import fib"
    print("Python code: ", timeit.timeit('fib_python(47)', setup=python_setup), "seconds")
    print("Cython code: ", timeit.timeit('fib.fib_cython(47)', setup=cython_setup), "seconds")
    print("Optimized Cython code: ", timeit.timeit('fib.fib_cython_optimized(47)', setup=cython_setup), "seconds")
    print("C code: ", timeit.timeit('fib.fib_c(47)', setup=cython_setup), "seconds")

輸出結果就會是下面這樣：

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C:\Users\*****\Miniconda3\envs\idp\python.exe D:/Dropbox/Data/programming/Python/Cython/1_fib/main.py
##### check result #####
fib(47) in python: 2971215073
fib.fib_c(47): 2971215073
fib.fib_cython(47): 2971215073
fib.fib_cython_optimized(47): 2971215073

##### performace benchmark #####
Python code:  2.9352622053858113 seconds
Cython code:  1.7331176511158422 seconds
Optimized Cython code:  0.14643933094340067 seconds
C code:  0.11884286952119272 seconds

Process finished with exit code 0